[phenixbb] phenix.rna_validate and the MolProbity web server report different bond angle violations

[Nathaniel Echols]

It took us a while to figure out what was supposed to happen here, but the
answer is that phenix.rna_validate is outdated and the numbers in
MolProbity are correct.  I'm fixing rna_validate now (and incorporating it
into the new phenix.molprobity framework).

-Nat


On Tue, May 13, 2014 at 6:23 AM, Huw Jenkins <h.t.jenkins at me.com> wrote:

> Hi,
>
> I’ve recently been using phenix.erraser to help correct RNA geometry
> errors and finding it very useful. However, it appears that the geometry
> validation statistics reported by phenix.rna_validate with respect to bond
> angle outliers are very different from those reported by the MolProbity web
> server.
>
> As an example - if I run phenix.rna_validate on 1u8d (as used in the
> documentation for phenix.erraser) the following outliers are reported:
>
> RNA Validation
> -----------------------------------------------
> Pucker Outliers:
> #residue:delta_angle:is_delta_outlier:epsilon_angle:is_epsilon_outler
>    G A  15 :74.054:no:103.458:yes
>    U A  48 :119.081:yes:283.965:no
>    U A  63 :90.366:yes:74.220:yes
>
> -----------------------------------------------
> Bond Length Outliers:
> #residue:atom_1:atom_2:num_sigmas
>
> -----------------------------------------------
> Angle Outliers:
> #residue:atom_1:atom_2:atom_3:num_sigmas
>    C A  39 : C5': C4': C3':-5.294
>    U A  63 : O3': C3': C2':-4.402
>
> -----------------------------------------------
> Suite Outliers:
> #suiteID:suite:suiteness:triaged_angle
>    G A  16 :!!:0.000:epsilon-1
>    U A  48 :!!:0.000:delta
>    U A  49 :!!:0.000:delta-1
>    A A  64 :!!:0.000:epsilon-1
>
> The MolProbity web server reports the same pucker and suite outliers but
> flags up many more angle violations:
>
> A 39             C      worst is C5'-C4'-C3': 10.588 σ
> A 63             U      worst is O3'-C3'-C2': 8.803 σ
> A 54             C      worst is C5'-C4'-C3': 7.883 σ
> A 49             U      worst is C2'-C1'-N1: 5.416 σ
> A 62             G      worst is C2'-C1'-N9: 4.946 σ
> A 15             G      worst is O3'-C3'-C2': 4.825 σ
> A 22             U      worst is C5'-C4'-C3': 4.785 σ
> A 64             A      worst is C4'-C3'-O3': 4.648 σ
> A 65             A      worst is C2'-C1'-N9: 4.582 σ
> A 44             A      worst is C4'-C3'-C2': 4.395 σ
>
> As the number of sigmas for the angle violations are different between
> phenix.rna_validate and MolProbity I guess they’re using different target
> distributions (not just reporting at a different sigma cut-off) but I’ve no
> idea which is more valid.
>
> Hopefully there is a simple explanation!
>
> Thanks,
>
>
> Huw
>
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